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Cadmium in PDB 4mt2: Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2

Protein crystallography data

The structure of Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2, PDB code: 4mt2 was solved by A.H.Robbins, C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 30.900, 30.900, 120.400, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / n/a

Other elements in 4mt2:

The structure of Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Sodium (Na) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2 (pdb code 4mt2). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2, PDB code: 4mt2:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 4mt2

Go back to Cadmium Binding Sites List in 4mt2
Cadmium binding site 1 out of 5 in the Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd62

b:26.0
occ:1.00
SG A:CYS60 2.5 24.2 1.0
SG A:CYS57 2.5 28.0 1.0
SG A:CYS59 2.5 26.2 1.0
SG A:CYS50 2.6 25.0 1.0
N A:CYS60 3.2 27.1 1.0
CB A:CYS57 3.4 30.2 1.0
CB A:CYS60 3.4 25.6 1.0
CB A:CYS59 3.4 26.6 1.0
C A:CYS59 3.6 27.1 1.0
CD A:CD65 3.7 27.2 1.0
CB A:CYS50 3.7 25.1 1.0
CA A:CYS59 3.8 27.2 1.0
N A:CYS59 3.9 28.6 1.0
CA A:CYS60 3.9 27.6 1.0
CD A:CD64 4.0 21.1 1.0
SG A:CYS37 4.1 23.6 1.0
CA A:CYS50 4.2 25.4 1.0
CG1 A:ILE49 4.2 20.4 1.0
O A:CYS59 4.5 27.2 1.0
N A:CYS50 4.5 23.6 1.0
CD1 A:ILE49 4.6 20.6 1.0
CA A:CYS57 4.8 31.6 1.0
C A:CYS57 5.0 31.0 1.0

Cadmium binding site 2 out of 5 in 4mt2

Go back to Cadmium Binding Sites List in 4mt2
Cadmium binding site 2 out of 5 in the Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd63

b:19.7
occ:1.00
SG A:CYS34 2.4 22.6 1.0
SG A:CYS48 2.5 18.8 1.0
SG A:CYS33 2.5 18.6 1.0
SG A:CYS44 2.6 19.5 1.0
CB A:CYS48 3.4 18.3 1.0
CB A:CYS34 3.4 0.0 1.0
O A:HOH96 3.6 16.9 1.0
CB A:CYS44 3.6 18.5 1.0
CB A:CYS33 3.7 18.9 1.0
CA A:CYS48 3.7 0.0 1.0
SG A:CYS50 3.9 25.0 1.0
C A:CYS33 4.0 20.1 1.0
N A:CYS34 4.0 20.4 1.0
CD A:CD65 4.0 27.2 1.0
CD A:CD64 4.2 21.1 1.0
O A:CYS33 4.3 20.6 1.0
CA A:CYS33 4.3 20.0 1.0
CA A:CYS34 4.3 21.8 1.0
N A:ILE49 4.4 20.5 1.0
C A:CYS48 4.5 19.5 1.0
N A:CYS50 4.6 23.6 1.0
CB A:CYS50 4.6 25.1 1.0
N A:CYS33 4.7 19.6 1.0
CB A:CYS37 4.8 23.6 1.0
N A:CYS48 4.8 17.8 1.0
SG A:CYS37 4.8 23.6 1.0
CA A:CYS44 4.9 17.9 1.0

Cadmium binding site 3 out of 5 in 4mt2

Go back to Cadmium Binding Sites List in 4mt2
Cadmium binding site 3 out of 5 in the Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd64

b:21.1
occ:1.00
SG A:CYS41 2.5 21.4 1.0
SG A:CYS44 2.5 19.5 1.0
SG A:CYS37 2.5 23.6 1.0
SG A:CYS60 2.6 24.2 1.0
CB A:CYS44 3.4 18.5 1.0
CB A:CYS37 3.5 23.6 1.0
CB A:CYS60 3.6 25.6 1.0
CB A:CYS41 3.6 20.6 1.0
CD A:CD65 3.8 27.2 1.0
SG A:CYS50 3.8 25.0 1.0
CD A:CD62 4.0 26.0 1.0
N A:CYS44 4.0 19.3 1.0
CD A:CD63 4.2 19.7 1.0
O A:HOH96 4.2 16.9 1.0
CA A:CYS44 4.3 17.9 1.0
SG A:CYS34 4.6 22.6 1.0
O A:HOH137 4.8 33.1 1.0
CB A:LYS43 4.8 20.0 1.0
C A:LYS43 4.8 19.7 1.0
CG1 A:ILE49 4.9 20.4 1.0
CA A:CYS37 4.9 23.4 1.0
O A:HOH101 4.9 40.8 1.0
CA A:CYS41 4.9 20.5 1.0
CA A:CYS60 5.0 27.6 1.0

Cadmium binding site 4 out of 5 in 4mt2

Go back to Cadmium Binding Sites List in 4mt2
Cadmium binding site 4 out of 5 in the Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd65

b:27.2
occ:1.00
SG A:CYS37 2.4 23.6 1.0
SG A:CYS36 2.5 27.4 1.0
SG A:CYS50 2.5 25.0 1.0
SG A:CYS34 2.5 22.6 1.0
CB A:CYS50 3.4 25.1 1.0
CB A:CYS37 3.4 23.6 1.0
CB A:CYS36 3.4 26.5 1.0
N A:CYS37 3.5 24.3 1.0
CB A:CYS34 3.6 0.0 1.0
C A:CYS36 3.7 25.5 1.0
CD A:CD62 3.7 26.0 1.0
CD A:CD64 3.8 21.1 1.0
CA A:CYS36 3.9 26.1 1.0
SG A:CYS57 4.0 28.0 1.0
CD A:CD63 4.0 19.7 1.0
CA A:CYS37 4.0 23.4 1.0
N A:CYS36 4.1 26.4 1.0
CB A:CYS57 4.1 30.2 1.0
O A:CYS36 4.3 26.4 1.0
SG A:CYS44 4.6 19.5 1.0
CA A:CYS50 4.7 25.4 1.0
SG A:CYS60 4.7 24.2 1.0
CA A:CYS34 4.9 21.8 1.0
O A:HOH120 4.9 36.8 1.0

Cadmium binding site 5 out of 5 in 4mt2

Go back to Cadmium Binding Sites List in 4mt2
Cadmium binding site 5 out of 5 in the Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd66

b:21.9
occ:1.00
SG A:CYS5 2.5 25.1 1.0
SG A:CYS21 2.5 22.5 1.0
SG A:CYS24 2.5 20.9 1.0
SG A:CYS7 2.5 22.5 1.0
CB A:CYS21 3.4 22.6 1.0
CB A:CYS24 3.5 19.9 1.0
CB A:CYS5 3.5 25.9 1.0
CB A:CYS7 3.6 21.9 1.0
CA A:CYS24 3.7 19.6 1.0
CA A:CYS5 3.8 26.5 1.0
ZN A:ZN68 3.8 22.6 1.0
ZN A:ZN67 3.9 18.6 1.0
N A:CYS7 3.9 22.4 1.0
N A:SER6 3.9 24.6 1.0
C A:CYS5 4.2 25.5 1.0
N A:LYS25 4.3 18.2 1.0
CA A:CYS7 4.4 21.8 1.0
SG A:CYS19 4.4 20.3 1.0
SG A:CYS26 4.5 23.0 1.0
CB A:CYS19 4.5 21.4 1.0
C A:CYS24 4.5 19.1 1.0
SG A:CYS15 4.7 21.8 1.0
C A:SER6 4.8 23.4 1.0
N A:CYS24 4.8 20.7 1.0
CA A:CYS21 4.8 23.2 1.0
CA A:SER6 4.9 24.2 1.0

Reference:

W.Braun, M.Vasak, A.H.Robbins, C.D.Stout, G.Wagner, J.H.Kagi, K.Wuthrich. Comparison of the uc(Nmr) Solution Structure and the X-Ray Crystal Structure of Rat Metallothionein-2. Proc.Natl.Acad.Sci.Usa V. 89 10124 1992.
ISSN: ISSN 0027-8424
PubMed: 1438200
DOI: 10.1073/PNAS.89.21.10124
Page generated: Sat Dec 12 08:25:12 2020

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